dbSNP rs1573815: STIMATE-MUSTN1:c.880-2367C>T (chr3-52836116-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_001198974.3(STIMATE-MUSTN1):c.880-2367C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,458 control chromosomes in the GnomAD database, including 4,876 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.25 ( 4864 hom., cov: 32)

Exomes 𝑓: 0.19 ( 12 hom. )

Consequence

STIMATE-MUSTN1
NM_001198974.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.66

Publications

19 publications found

Variant links:

Genes affected

STIMATE-MUSTN1 (HGNC:38834): (STIMATE-MUSTN1 readthrough) This locus represents naturally occurring read-through transcription between the neighboring TMEM110 (transmembrane protein 110) and MUSTN1 (musculoskeletal, embryonic nuclear protein 1) genes. The read-through transcript encodes a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Nov 2010]

STIMATE-MUSTN1 links:

STIMATE (HGNC:30526): (STIM activating enhancer) Enables calcium channel regulator activity. Involved in activation of store-operated calcium channel activity; calcium-mediated signaling using intracellular calcium source; and positive regulation of calcineurin-NFAT signaling cascade. Located in cortical endoplasmic reticulum; endoplasmic reticulum membrane; and endoplasmic reticulum-plasma membrane contact site. [provided by Alliance of Genome Resources, Apr 2022]

STIMATE links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.43).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001198974.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STIMATE-MUSTN1	NM_001198974.3		c.880-2367C>T		intron	N/A	NP_001185903.2	A8MSY1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
STIMATE-MUSTN1	ENST00000504329.1	TSL:5	c.880-2367C>T	intron	N/A	ENSP00000422941.1	A8MSY1
STIMATE-MUSTN1	ENST00000514466.5	TSL:2	c.247-1113C>T	intron	N/A	ENSP00000422189.1	H0Y8V1
STIMATE-MUSTN1	ENST00000495552.1	TSL:2	n.4147C>T	non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.246

AC:

37382

AN:

151912

Hom.:

4864

Cov.:

show subpopulations

Gnomad AFR

AF:

0.210

Gnomad AMI

AF:

0.401

Gnomad AMR

AF:

0.374

Gnomad ASJ

AF:

0.313

Gnomad EAS

AF:

0.322

Gnomad SAS

AF:

0.128

Gnomad FIN

AF:

0.259

Gnomad MID

AF:

0.236

Gnomad NFE

AF:

0.234

Gnomad OTH

AF:

0.244

GnomAD4 exome

AF:

0.193

AC:

AN:

430

Hom.:

Cov.:

AF XY:

0.176

AC XY:

AN XY:

238

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.188

AC:

AN:

South Asian (SAS)

AF:

0.100

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.143

AC:

AN:

294

Other (OTH)

AF:

0.375

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.246

AC:

37409

AN:

152028

Hom.:

4864

Cov.:

AF XY:

0.248

AC XY:

18439

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.210

AC:

8710

AN:

41448

American (AMR)

AF:

0.374

AC:

5705

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.313

AC:

1085

AN:

3470

East Asian (EAS)

AF:

0.321

AC:

1656

AN:

5152

South Asian (SAS)

AF:

0.129

AC:

620

AN:

4824

European-Finnish (FIN)

AF:

0.259

AC:

2741

AN:

10580

Middle Eastern (MID)

AF:

0.233

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.235

AC:

15939

AN:

67968

Other (OTH)

AF:

0.246

AC:

519

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1444

2887

4331

5774

7218

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

376

752

1128

1504

1880

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.267

Hom.:

1041

Bravo

AF:

0.257

Asia WGS

AF:

0.238

AC:

826

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.43

CADD

Benign

(source)

DANN

Benign

0.79

PhyloP100

1.7

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over